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clonalframeml website  

ClonalFrameML is a software package that performs efficient inference of recombination in bacterial genomes.

ClonalFrameML can be applied to any type of aligned sequence data, but is especially aimed at analysis of whole genome sequences. It is able to compare hundreds of whole genomes in a matter of hours on a standard Desktop computer. There are three main outputs from a run of ClonalFrameML: a phylogeny with branch lengths corrected to account for recombination, an estimation of the key parameters of the recombination process, and a genomic map of where recombination took place for each branch of the phylogeny.

Required Modules


  • clonalframeml

System Variables

  • HPC_CLONALFRAMEML_DIR - installation directory


If you publish research that uses clonalframeml you have to cite it as follows:

Didelot X, Wilson DJ (2015) ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes. PLoS Comput Biol 11(2): e1004041. doi:10.1371/journal.pcbi.1004041.


  • Validate 4/5/2018